How much are you putting in the hvac budget?
whatever the minimum is to make it cool/warm and not cost shitloads to do so.
Top floor: 15-18 SEER two stage heat pump with air handler
First Floor / Basement: 15-18 SEER two stage ac with two stage condensing gas furnace and zoning.
You can always save some money by using single stage equipment and dropping to 13 SEER efficiency. However you lose some comfort.
As far as brands go, you'll have to go with whatever your builder's subcontractor uses unless you can buy your own.